Step 1: You can confirm the duplicate account the customer created by resetting the password on the duplicate account. (The account needs to be confirmed before you can manipulate it)
Step 2: Once the duplicate account in mission control has been confirmed, you can then change the phone number on the duplicate account to a dummy/bogus phone number of any kind. (That frees up the number so it can be added to the original customer account)
Step 3: Go to the original customer account and you can now update the customer phone number since its not being used by the duplicate account they created.